To quantify the effect of Zoumatang drainage on the water quality of Wangyu River after the transfer of water diversion project, a two-dimensional mathematical model of water environment for the Jiangsu section of Yangtze River is established, and TP is selected as the research object, and the influence of Zoumatang drainage on the water quality of Wangyu River diversion entrance under different schemes is quantified. The water quality improvement measures in the later stage of diversion were put forward. The results showed that the effect of Zoumatang River drainage on the water quality of Wangyu River diversion was affected by tidal fluctuation, and the maximum increase of TP concentration of Wangyu River diversion water quality could reach 21.3% after the entrance of the diversion project was moved outside. Improving the drainage quality of Zoumatang can reduce the impact on the water quality of Wangyu River Diversion Project. It is more obvious to decrease the concentration of total phosphorus in Wangyu River by the way of interval water diversion. When the water diversion is done after the water quality of Zoumatang reaches the standard of surface water environment IV and the drainage is stopped for 48 hours, the increase of total phosphorus concentration can be basically controlled below 1%.